Elder was appointed music director of the Hallé Orchestra in 1999.[6] His first concert as music director was in October 2000.[7]

He proposed several novel ideas for concerts. These have included the abandonment of traditional concert evening garb.[8] Elder is generally regarded as having restored the orchestra to high musical standards, after a period where the continuing existence of the orchestra was in doubt.[9] In 2004, he signed a contract to extend his tenure from 2005 to 2008, with an optional two-year extension at the end of that time.[10] A 2005 report indicated that Elder would be with the orchestra at least until 2010.[11]

In May 2009, the orchestra announced the extension of Elder's contract to 2015.[12] In November 2013, the Hallé announced the further extension of Elder's contract through "at least 2020".[13][14] He has been President of the London Philharmonic Choir from 2014 to the present.

He first conducted the Last Night of the Proms in 1987. He was scheduled to conduct again in 1990, but his remarks about the nature of some of the traditional Proms selections in the context of the impending first Gulf War led to his dismissal from that engagement.[15] In 2006, he returned to conduct the BBC Symphony Orchestra for his second "Last Night" engagement, and used the traditional speech at the end of the concert to criticise aircraft baggage restrictions, in place following the uncovering of the 2006 transatlantic aircraft plot, which have made it difficult for musicians to carry their instruments on aircraft.[16] In a reference to the fact that laptop computers are now allowed in aircraft cabins, Elder said, "...it seems to me that next year we should all look forward to 'Concerto for Laptop and Orchestra.'"[17][18] He also made a plea for children to be given more opportunity to sing at school.[19]

Elder was appointed Commander of the Order of the British Empire (CBE) in the 1989 Queen's Birthday Honours.[20] He won an Olivier Award in 1991 for his outstanding work at English National Opera. He received the 2006 conductor prize of the Royal Philharmonic Society.[21] In April 2007, Elder was one of eight conductors of British orchestras to endorse the 10-year classical music outreach manifesto, "Building on Excellence: Orchestras for the 21st Century", to increase the presence of classical music in the UK, including giving free entry to all British schoolchildren to a classical music concert.[22] Elder received a knighthood in the Queen's Birthday Honours of June 2008.[23][24]

In addition to being involved in the above-named orchestras, Elder became "principal artist" of the Orchestra of the Age of Enlightenment in December 2011.[25] As noted in the article: "His first project with the OAE as principal artist was [to give] a performance of Berlioz's Romeo and Juliet on 18 February 2012 at the Royal Festival Hall, London."

Describing his own conducting style, Elder has said that in contrast to Sir Adrian Boult, who was famously non-perspirational:

I'm quite a physical conductor. I remember seeing Adrian Boult backstage after the 1978 Proms and he was wearing a freshly ironed light blue M&S shirt and he said to me "I see you're one of the sweaty ones."[26]

Elder has recorded for the Hyperion, NMC, Chandos, Opera Rara, and Glyndebourne record labels, as well as for the Hallé Orchestra's own label. In addition to his conducting and recording activities, Elder also has written on music for The Guardian and other newspapers.[27]